Crystallography Open Database





 
What's New ?

 
  • November 2014: The "FPSM method" uses a Rietveld like fitting procedure to test all possible crystal structures from the Crystallography Open Database, rank them and find the more probable in your diffraction pattern. In the end a Rietveld phase quantification is done with the phases identified. The new paper is sumitted to the J. Appl. Cryst.

  • November 2014: The new QUALX version has been developed that can use COD data for search-match material identification.

  • October 2014: PANalytical publishes a new release of their COD-derived search-match database. The new COD database file is meant to be used with version 3.0e or higher of the PANalytical HighScore or HighScore Plus software packages. It can be downloaded in two parts of ~ 1.4 Gb each from the archive.

  • August 2014: COD is added to the list of recommended data repositories by the Nature Publishing Group journal Scientific Data.

  • August 2014: COD and TCOD were presented in a poster session of the 23rd Congress and General Assembly of the IUCr in Montreal, Canada. The posters are stored in the COD archives.

  • January 2014: During the visit of Peter Murray-Rust in the University of Vilnius, Institute of Biotechnology, the COD was merged with the data from CrystalEye, and started using Jumbo Converters to generate lists of chemically interesting moyeties and fragments. These lists are stored in the COD data directory, and will soon be available as an SQL database and via the Web interface.

  • April 2014: Two RSS feeds for exploring the COD have been launched: "What's New on COD" and "New Structures in COD". Both feeds should be automatically detectable at COD Home page. For browsers that do not support RSS, COD feeds can be accessed using web-based feed viewers like FeedBucket: "What's New on COD" and "New Structures in COD".

  • November 2013: Structure preview using JSmol, JavaScript-only alternative of Jmol, is implemented in CIF information cards. Now preview of COD structures is available on the platforms that do not support Java (i.e. iPhone/iPad) or do not support applets (i.e. Android). Structure preview using Jmol is still available via link 'Display in Jmol' below the JSmol view.

  • September 2013: Rigaku issues a new search-match database with powder patterns from COD.

  • June 2013: PANalytical publishes a new release of the COD-derived search-match database. The new COD database file is meant to be used with version 3.0a or higher of the PANalytical HighScore or HighScore Plus software packages.

  • March 2013: Search engine plugin for Firefox and IE7 Web browsers for querying the COD is now available. When installed, the plugin places COD among the browser's search engines (in Firefox 14.0.1, they are accessible in the drop down list in the top-right corner of the brower's window). The plugin allows querying the COD via textual and COD ID searches. The plugin is based on OpenSearch description format, which is compatible with Firefox and IE7 (we haven't tested the latter yet). Firefox comes with autodiscovery feature, so to obtain the plugin, please visit www.crystallography.net and the option "Add COD" should appear in the browser's drop down menu containing search engines.

  • February 2012: a new edition of the COD database for search-match and structure retrieval with PANalyticals HighScore and HighScore Plus software is available now!

  • September 2011: Corrected COD database for search-match and structure retrieval with PANalyticals HighScore and HighScore Plus software is available now!

  • July 2011: Powder patterns for the Rigaku software are updated!

  • January 2011: Powder patterns computed from COD are available for Rigaku software.

  • December 2007 : Further developments of the COD (and PCOD) will take place in Lithuania, supervised by Dr. Saulius Gra┼żulis, Institute of Biotechnology, Graiciuno 8, LT-02241 Vilnius, Lietuva (Lithuania), and a student, Justas Butkus, from the Vilnius  Gediminas Technical University. 
    New Web address : http://cod.ibt.lt/

  • September 2007 : at its recent meeting the IUCr Executive Committee decided that the CIFs associated with structural papers published in IUCr journals should be made freely available to the databases, including COD. Thus COD has permission to download these files from the IUCr site on a routine basis.

  • February 2007 : Creation of the P2D2 ; Predicted Powder Diffraction Database

  • 61015 entries - search-match possible with the EVA Bruker software
  • February 2007 : Massive PCOD update

  • 58500 entries added, see details
    61132 total in PCOD
  • December 2006 : COD update : ~48000 entries (~10000 from AMCSD)
  • June 2006 : COD update : ~43000 entries
  • May 2006 : COD update : ~40000 entries
  • April 2006 : COD update : ~37000 entries (~9000 from AMCSD)
  • March 2006 : COD update : ~34000 entries
  • February 2006 : PCOD update with >1000 predicted titanosilicates : ~2600 entries (total)
  • January 2006 : COD update : ~31000 entries
  • December 2005 : COD update : ~28000 entries
  • November 2005 : COD update : ~24000 entries
  • October 2005 : COD update : ~20000 entries
  • ~30 Volunteers declared wanting to help 
  • New COD Advisory Board Members 
  • Call to volunteers
  • September 2005 : COD update : ~18000 entries (~8000 from AMCSD)
  • August 2005 : poster presented at the IUCr XX, Florence
  • June 2005 : more than 1000 signatures to the petition.
  • May 2005 :  Petition for Open Data in Crystallography
  • Asked for permission to ACS to copy systematically their CIF files.
  • Still no permission to copy the CIF files availaible for free at the Acta Cryst. journals Web pages.
  • May 2004, EMC2, El Jadida, Morocco, conference (in French) on databases (powerpoint file) - were assisting : Bill Duax as IUCr President, Claude Lecomte as former ECA President. Both agreed that the PDB should be considered as a model, with open access on the Web (pictures).
  • January 2004 : added ~200 new entries in the PCOD (B2O3, AlF3, BxSiyOz, BxReyOz and SixReyOz

  • predicted - or enumerated - by GRINSP with R(DLS)< 0.01 
  • January 2004 : added ~ 400 new entries from AMCSD (5448 entries from AMCSD, total entries : 12965)
  • December 2003 : a subset of the COD is created : PCOD (Predicted Crystallography Open Database). This is an attempt to gather all these theoretical crystal structures which will very probably soon exceed in number the really observed ones. 
  • November 2003 : added ~300 new CIFs from AMCSD
  • September 2003 : the COD query for accessing or having a link towards the IUCR CIFs failed (read the query and the answer).
  • Conference on Open Access to the Data and Results of the Sciences and Humanities

  •      20 - 22 Oct 2003, Berlin -  http://www.zim.mpg.de/openaccess-berlin/index.html
  • August 2003 : a tutorial is written describing how to install the COD on your own computer (PC) and running it in standalone conditions.
  • July 2003 : The July 2003 2nd edition of the on-line IUCr Computing Commission Newsletter on-line is available as an Acrobat PDF file (~2.6Meg and 57 pages) at : http://www.iucr.org/iucr-top/comm/ccom/newsletters/2003jul/

  • See inside a contribution about COD : 
    "How easy/hard is to convert raw data into a web database? - by  Armel Le Bail 
  • July 2003 : Crystal Impact, sponsor at the beginning (through Michael Berndt, offering the www.crystallography.net domain name) disengaged from the COD. The domain name is transferred under the control of the COD.
  • Sad news about one of the main COD initiators, Michael Berndt.

  • By email from Dr. Klaus Brandenburg and Dr. Holger Putz : 

    Michael Berndt died on June 30th, 2003 after a long, serious illness at the age of 39. 

    Michael studied chemistry and received his PhD in 1995 in the group of Prof. Bergerhoff at the university of Bonn, Germany. Even during his studies he was active in writing chemistry software. For the retrieval software of the Inorganic Crystal Structure Database (ICSD), he won the German-Austrian Academic Software Award in 1993. In 1997, he founded the company Crystal Impact together with Dr. Klaus Brandenburg. Michael was substantially involved in the development of the Browser software for the Inorganic Materials Database "Pauling File". Based on his long-term experience in this area, he started with a new, universally applicable system for the simultaneous access to diverse crystallographic databases. 

    With Michael we lose an always competent, reliable and helpful colleague. 
     

  • May 2003 : 200 REF files added, mainly taken from the SDPD database of references - Much more to come. The REF files can be completed with atomic coordinates and transformed into CIFs by the REF2CIF software.
  • May 2003 : CIFs do not have to be located at the COD server side. If there is a CIF available somewhere in the Internet, the COD can provide a link to it. Thus, we have created an option for datasets, called REF files, that operate like a pointer. They contain minimal information, allowing a search for cell parameters, volume, chemical formula, reference including text in publication title, authors, journal, year. Therefore, one can now deposit either CIF (preferably) or REF files to the COD. A REF file is quite simple to make by a text editor. It contains 4 lines :

  • 1- reference as complete as possible (or/and comments if any) 
    2- chemical formula with spaces (ex : C2 H6 O) 
    3- the 6 cell parameters in angstroms and dregrees : a b c alpha beta gamma separated by one space 
    4- space group in Hermann Mauguin notation, no space 
    A REF file can contain a series of 4 lines (references + minimal crystal data) separated by an empty line. 
    Example for 2 entries in the same REF file :

    A.J. Mora, A.N. Fitch, The low-temperature crystal structure of RS-camphor, J. Solid State Chem 134 (1997) 211-214
    C10 H16 O
    6.8341 11.6584 11.5000 90. 90. 90.
    Cmcm

    C. Feldmann, M. Jansen, To the knowledge of cis-sodium hyponitrite, Z. Anorg. Allg. Chem. 623 (1997) 1803-1809
    Na2 N2 O2
    5.107 9.211 6.159 90. 97.91 90.
    P21/c

    The REF files will be built very easily from your own list of publication references with addition of the chemical formula, the cell parameters and the space group. 
     

  • April 2003 : The IUCr is contacted for permission of downloading the IUCr journals freely available CIFs. Decision will be taken by the Executive Committee in August 2003. As a test, the Acta Cryst. C 1991 and 1992 references + minimal crystal data pointing at the IUCr existing CIFs are included in COD. The search result redirects to the IUCr journals web site. 
  • April 2003 : Donation of > 1200 CIFs from IPMC. Thanks ! 
  • March 2003 : A new Web page showing the logos with links to the main Donators is set up.
  • March 2003 : Donation of > 850 CIFs from the CRISMAT (Caen, France). Thanks !
  • March 2003 : First minimal search page coded in PHP.
  • March 2003 : Donation of 450 CIFs from the Laboratoire des Fluorures (Le Mans, France). Thanks !
  • March 2003 : Donation of 3725 CIFs from the American Mineralogist database (Bob Downs). Thanks a lot !
  • March 2003 : The CIF2COD program (FORTRAN) is built up on the basis of CIF2SX from Louis Farrugia. Thanks ! CIF2COD read several CIFs (from n.cif to n+m.cif), performs several quality tests, and produces a .txt file containing m+1 lines with the MySQL database (cod) unique table (data) fields (entry, file, pdf, a, b, c, alpha, beta, gamma, vol, nel, sg, formula, text).
  • March 6, 2003 : The CryOD Mailing List is open to the COD Advisory board members.
  • March 5, 2003 : COD birth (announced at various mailing lists, Newsgroups, and IUCr What's New Web page), starting after a discussion at the SDPD Mailing List (February 12-14, 2003) and the writing of the crystallography database quiz (removed now) - see various early emails.

  •  
  • Introductory text : Databases of crystal structure atomic coordinates (most of them commercial databases) delay new data by 3, 6 months, if not much more (1, 2 years) after the publication. As a crystallographer, you certainly are interested in having access as soon as possible to new and old data, and why not for free. Your main reason can be that you do not want to waste time in a structure redetermination of an already known compound. The Internet offers possibilities for quasi immediate answers, provided :

  • 1. A small team of engaged scientists with some experience in database and software design coordinate the Crystallography Open Database (COD) project based on free and automated software a) for maintaining the database, b) for data evaluation and calculation of derived data (e.g. calculated powder pattern from crystal structures for search-match purposes), c) for browsing and retrieval. 
    2. The authors (i.e. the scientific community = YOU) provide the project with database entries (note, that if you have'nt sold your experimental results exclusively, you are free to distribute the data to such a database, even if they have already been part of a publication - and a lot of good data have never been published). 

    We are not in the same situation as decades before when the well-known databases (ICSD, CSD, PDF) started. Today we have the Internet, fast computers, and a big pool of free available software. The question is : Do we have enough scientists who are willing to cooperate ? 
    The COD, once finalized, will be nothing else than a keyword-searchable Web server of crystal structure atomic coordinates, preserving the data after publication as well as unpublished data. 
     

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